In Bioconductor/HCAMatrixBrowser: Extract and manage matrix data from the Human Cell Atlas project

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
options(tibble.print_min = 5, tibble.print_max = 5)

HCAMatrixBrowser

Overview

HCAMatrixBrowser gives users access to the matrix download service for the Human Cell Atlas project.

It provides a main function for downloading data matrices from either a set of bundle_fqids or a data filters.

• loadHCAMatrix allows either a vector of bundle_fqids or an added filter operation to the HCA API object

API object

library(HCAMatrixBrowser)

hca <- HCAMatrix()

Quick Start

with bundle_fqids

my_fqids <-
    c("ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775.2019-05-14T122736.345000Z",
    "f69b288c-fabc-4ac8-b50c-7abcae3731bc.2019-05-14T120110.781000Z")

loadHCAMatrix(hca, bundle_fqids = my_fqids)

with filter operations

hca1 <- filter(hca, bundle_uuid == "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775")
## filter print out
filters(hca1)

loadHCAMatrix(hca1)

Bioconductor/HCAMatrixBrowser documentation built on March 16, 2023, 6:16 a.m.